Alternative splicing of pre-mRNA

Energy-dependent alternative splicings 1996 – 2016 (2)

See also: Energy-dependent alternative splicings 1996 – 2016

Re: Rs3827760 is Val370Ala and EDARV370A

No matter what it is called, Val370Ala may be the best example of how nutrient energy-dependent biophysically constrained pheromone-controlled viral latency protects all organisms from virus-driven energy theft and all pathology.
For example, see: Genome recoding by tRNA modifications

The succession of mRNA codons controls the synthesis of polypeptides through the complementarity between each of the 64 possible codon triplets and the tRNA anticodons that decode the 20 amino acids of the cellular proteome. Central to the mRNA decoding process is the backward compatibility of the codon : anticodon recognition that is mediated by tRNA.

See also: In the loop: how chromatin topology links genome structure to function in mechanisms underlying learning and memory

Highlights:

•    Epigenetic regulation represents a key mechanism of learning, memory and cognition.
•    Chromatin topology is emerging as a major regulator of neuronal gene expression.
•    Dynamic chromatin topology changes correlate with activity-dependent transcription.
•    DNA double-strand breaks facilitate induction of immediate early gene transcription.

All their highlights can be placed into the context of this article from 2005.
Feedback loops link odor and pheromone signaling with reproduction
The feedback loops determine whether of not a species survives via links from energy-dependent autophagy to learning, memory, RNA-mediated amino acid substitutions and supercoiled DNA.
BDNF Val66Met and COMT Val158Met are also examples that link energy-dependent changes in base pairs from single nucleotide polymorphisms to life history transitions in morphological and behavioral phenotypes.

See also: Spatiotemporal antagonism in mesenchymal-epithelial signaling in sweat versus hair fate decision

Our findings revealed a differential impact of BMP signaling on appendage fate specification that has ancient roots and occurs repeatedly throughout vertebrate evolution.

This was reported by Bob Yirka as: Researchers identify signals during embryonic development that control the fate of skin cells to be sweaty or hairy

The fate of all cell types is energy-dependent and RNA-mediated via natural selection for codon optimality. See for example:
rs3827760, also known as 1540T/C, 370A or Val370Ala, is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2. This SNP links the mouse model of cell type differentiation to humans. That fact has been known for at least 3 years.
See:

  1. Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant
  2. A genetic basis of variation in eccrine sweat gland and hair follicle density
  3. A genome-wide association scan implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in human facial variation

Other energy-dependent base pair changes link natural selection for codon optimaility from SNPs to RNA-mediated amino acid substitutions and differences in intelligence and/or unexplained death risk.
A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence
An insertion/deletion polymorphism within 3’UTR of RYR2 modulates sudden unexplained death risk in Chinese populations
Few people can place the findings on energy-dependent codon optimaility into the proper context of natural information processing. How many do you know who might claim that natural selection links mutations to evolution?

Compare the people who think in terms of mutation-driven evolution to those who know the energy-dependent differences between archaea and bacteria. The greater energy-dependent stability of organized genomes in bacteria can be liked to the stability of eukaryotes. The instability of archaea genomes can be linked from virus-driven energy theft to the degradation of messenger RNA and negative supercoiling of DNA.
All cell type stability link the sun’s anti-entropic virucidal energy from the creation of all biodiversity to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy, which links mutations to all pathology.
See for instance, (2013) MicroRNA-based regulation of epithelial-hybrid-mesenchymal fate determination

The authors

…address long-standing fundamental questions linked to compelling clinical needs—how to distinguish between the aberrant dynamics of epithelial–hybrid–mesenchymal transitions during tumorigenesis vs. the normal programs of embryonic development and tissue regeneration.

The “normal programs” are energy-dependent and biophysically constrained by the physiology of reproduction.The senior author should have received the 2016 Nobel Prize for linking energy-dependent autophagy to supercoiled DNA, but the Prize is not awarded posthumously, as I recall.

Politicized “science” often prevents the Prize in Physiology or Medicine from being awarded to anyone whose works challenge the ridiculous theories about mutation-driven evolution. Those who present experimental evidence of how cell type differentiation is biophysically constrained by energy-dependent changes in the microRNA/messenger RNA balance tend to be virtually ignored.

Even some of the creationists I have encountered want others to keep thinking in terms of evolution rather that energy as information. Peter Berean, for example, decided to invent the term “bio-functional information” when he realized that the sun’s anti-entropic virucidal energy was the only obvious link from microRNA flanking sequences to all healthy longevity and that virus-driven energy theft was the link to all pathology.If you want to learn how serious scientists are combating evolution to fight disease on two fronts, see any claim made by an old earth creationist, or any claim made by any atheist. The similarities led Peter Berean to substitute “bio-functional information” for de Vries 1902 definition of “mutation.”

See for comparison:

2003 Bacterial self–organization: co–enhancement of complexification and adaptability in a dynamic environment

2006 Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information

2009 Learning from Bacteria about Natural Information Processing

See also: CRISPR study reveals unexpected roles of non-coding RNAs

Royal Society’s Sir Venki Ramakrishnan Agrees to Post Public Evo Audio

…the public discussion from the recent “new trends” in evolution conference will be posted shortly online on the Royal Society event webpage.

Suzan Mazur helped force them to do what they claim they would do:

Recorded audio of the presentations are available below.

It’s been six weeks and the recorded audios from the audience are not available.

If the recorded comments become available, the public discussion may help to reveal that the fate of all cell types is energy-dependent and RNA mediated via natural selection for codon optimality and autophagy.

See for other examples: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

These two reports (Grossman et al., 2013; Kamberov et al., 2013) tell a new short story of adaptive evolution. The story begins with what was probably a nutrient-dependent variant allele that arose in central China approximately 30,000 years ago. The effect of the allele is adaptive and it is manifested in the context of an effect on sweat, skin, hair, and teeth. In other mammals, like the mouse, the effect on sweat, skin, hair, and teeth is due to an epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates as previously indicated. That means the adaptive evolution of the human population, which is detailed in these two reports, is also likely to be nutrient-dependent and pheromone-controlled, since there is no other model for that.

Each week’s science news brings additional representations of facts that refute all neo-Darwinian pseudoscientific nonsense by linking Darwin’s “conditions of life” to all biodiversity. Most science news outlets still report and/or tout pseudoscientific nonsense because the reporters missed the fact that life is nutrient-dependent and the physiology of reproduction is controlled by pheromones is species from microbes to humans.
Can you imagine how embarrassed you would be if you had not learned that all organisms must eat or they cannot reproduce, which means they could never have become an organism of a species? What’s worst is that no experimental evidence of biologically-based cause and effect support claims that one species evolved into another. For comparison, this recent report shows changes in organized genomes that link the nutrient-dependent pheromone-controlled physiology of reproduction in moths to bacteria and from bactreria to humans via conserved molecular mechanisms of RNA-mediated protein folding chemisrty.

Engineers create programmable silk-based materials with embedded, pre-designed functions

… the researchers created a surgical pin that changes color as it nears its mechanical limits and is about to fail, functional screws that can be heated on demand in response to infrared light, and a biocompatible component that enables the sustained release of bioactive agents, such as enzymes.

The news article cites: Directed self-assembly of silk fibroin into bulk materials: with the subtitle: Programming function into mechanical forms from the nano- to macroscale,
I look forward to learning why they are claiming that energy-dependent assembly is “directed self-assembly.”

Alternative splicing of pre-mRNA

Re-inventing mutation-driven evolution

Peter Berean is an administrator of “The Battlefield” Facebook group.
He repeatedly claims that I have not proved that energy is information. For comparison, there is something he calls “bio-functional information.” He has not defined that term or placed it into the context of energy-dependent creation or into the context of evolutionary theory.
 
We have reached an impasse.
Simply put, he makes claims that are based on definitions without defining his terms. That forces others to return to the beginning of the 20th century, which is when de Vries defined the term “mutation.”
 
The assumptions of population geneticists led to ridiculous claims about mutations and evolution. Those claims have never been supported by experimental evidence of biologically-based cause and effect.
Many people are familiar with the rest of that “Just-So” story. Simply put, pseudoscientists bastardized Darwin’s theory, which was based on the creation of energy-dependent “conditions of life.”
 
If Peter Berean would simply tell us who created bio-functional information or where it came from if it was not created, his claims about creation and/or evolution could be discussed. The discussions might begin to include the virus-driven theft of quantized energy, which is the cause of all pathology.
 
I claim that Peter Berean cannot  cite any experimental evidence of biologically-based cause and effect that suggests bio-functional information is not energy as information. I claim that he knows his beliefs and the beliefs of many others rely on ongoing obfuscation of facts about energy as information.
 
I claim that the difference between people like Peter Berean and me is clear. I support my claims with experimental evidence of biologically-based cause and effect. I was taught to do that by experts who know that epigenetically-effected gene activation is energy-dependent and biophysically constrained by the physiology of reproduction.
 

There is no way to know what Peter Berean was taught, or why he appears to believe in people who taught him to believe in their pseudoscientific nonsense about evolution.

There are only example of ecological variation that have been linked to ecological adaptations in species from microbes to humans via conserved molecular mechanisms.

See: Rainbow snake, tiny frog among new Mekong species

Each year scientists announce new species, after an often lengthy identification process, highlighting how much more there is to learn about the region.

With each new variant it becomes clearer that all biodiversity is energy-dependent and biophysically constrained by the physiology of reproduction in the context of the innate immune system and supercoiled DNA, which protects all organized genomes from virus-driven energy theft.
The rainbow snake, for example, can be compared to the fruit dove as an example of nutrient energy-dependent pheromone-controlled biodiversity. The fossil record cannot be compared to anything known about energy-dependent biophysically constrained biodiversity. With the exception of what might be natural fluorescence in dinosaur osteocytes, all the energy-dependent variation seems to be missing from the fossil record. The nutrient-dependent pheromone-controlled weekend resurrection of the bacterial flagellum in P. fluorescens attests to that fact.
So does this report on nematodes. Worms Developed as Research Model for Microbiome & Disease

They linked the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria to biodiversity in two nematode species and claim that one of them evolved into a predatory nematode with teeth during the past 200 million years.
The neurobiological consequence of predating or grazing

“The patterns of synaptic connections perfectly mirror the fundamental differences in the feeding behaviours of P. pacificus and C. elegans”, Ralf Sommer concludes. A clear-cut result like that was not what he had necessarily expected. Previous studies in much simpler neural circuits – as in the marine snail Aplysia – had indicated that changes in behaviour do not have to coincide with changes in number and location of synapses. Differences in physiological properties of neurons or in their modulation by neurotransmitters can be sufficient to effect behavioural changes.

For comparison, see the article by Taylor et al on the weekend resurrection of the bacterial flagellum in P. fluorescens. Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
If you have ever worked in a medical laboratory and still believe in the pseudoscientific nonsense about millions of years of evolution, I hope you are not helping people like Peter Berean to kill people with your ridiculous beliefs about energy-dependent biologically based cause and effect.

Biology to a Physicist

Bird-brained theorists

Study: There Are Twice as Many Bird Species as Previously Estimated
The issue of biodiversity in all vertebrates was linked from ecological variation to nutrient energy-dependent ecological adaptation by natural selection for codon optimality and differences in morphology paired with differences in behavior in the context of the physiology of reproduction and biophysically constrained cell type differentiation.
See: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes

…our results illustrate a detailed chain of events linking a chromosomal rearrangement to changes in overt social behavior.

Thomas Hunt Morgan (1933-Medicine) and Schrodinger/Dirac (1933-Physics) collectively linked chromosomal rearrangements to all biophysically constrained biodiversity via their Nobel Prize-winning works.

Alternative splicing of pre-mRNA

Autophagy is the antiphage defense strategy

The “Antiphage Defense Strategy” in Vibrio anguillarum is called autophagy by many serious scientists. It links nutrient energy-dependent pheromone-controlled quorum sensing to viral latency, healthy longevity, symbiosis, reproduction, and biodiversity from microbial species to humans.

For an evolutionary approach to energy-dependent autophagy that fails to address any aspect of how virus-driven energy theft causes all pathology see: (12/7/16) Part I: Living together: The symbiosis of host-microbial interactions (12/7/16)
See also: 12/7/16

….McFall-Ngai tells the story of a symbiosis between the Hawaiian bobtail squid and Vibrio fischeri (V. fischeri), a type of luminescent bacteria that enables the squid to hunt at night. McFall-Ngai and collaborators have identified the molecular mechanism by which nascent Hawaiian bobtail squid select V. fischeri from the thousands of other bacteria in their habitat. V. fischeri induces developmental changes in the squid that drive daily rhythms of gene expression, which are necessary to control bacterial growth, a crucial cycle in this symbiotic partnership.


Bobtail squid select bacteria that become luminescent. The squid do not not select archaea. That fact exemplifies how natural selection for energy-dependent codon optimality links top-down causation from the sun’s anti-entropic biological energy to ecological adaptation.
Whether or not you accept this fact, energy-dependent natural selection continues in the context of symbiosis among the most ecologically adapted species.
“The four stages of acceptance: ― J.B.S. Haldane
1. This is worthless nonsense.
2. This is an interesting, but perverse, point of view.
3. This is true, but quite unimportant.
4. I always said so.”

Natural selection cannot link mutations to evolution in the context of symbiosis because the interactions among species are far too complex.

…the pattern of microbial exchange is “likely circular in nature.” That means that captive dragons contribute microbes to their environment, and they reacquire these same microbes from their environment, repeating this exchange in an ongoing cycle without other external sources of microbial diversity.

Pattern recognition is essential to the understanding of how the microbiome of bobtail squid is linked to symbiosis via the microbiome in all other living genera via the anti-entropic virucidal energy of sunlight.

Search Results for “McFall-Ngai”

Beneficial microbes kill beneficial mutations
1/15/15 Excerpt: McFall-Ngai, Bonnie Bassler, Anna Di Cosmo and others, continue to show that Darwin’s ‘conditions of life’ are nutrient-dependent and pheromone-controlled by linking:
1) metabolic networks,
2) genetic networks,
3) reproduction in microbes,
and
4) reproduction in their model organisms.

Environment epigenetically shapes the immune system
1/15/15 Excerpt: 1) –with my emphasis Re: “There’s nothing here that is revolutionary or requires rethinking of our assumptions about how the immune system functions…”
Quantum physics, quantum biology, and quantum consciousness
2/15/15 Excerpt: One would think that the representations of McFall-Ngai that appear to link light-induced amino acid substitutions from the stability of DNA in luminescent microbes to the stability of DNA in squid would invite more attention to details than attempts to pirate ideas about epigenetic links from Turin’s links and my links from quantum physics to Gunther Witzany’s Life is physics and chemistry and communication.

8/25/15 Excerpt: See also my invited review of nutritional epigenetics. I submitted it by request for a special issue of “Nutrients” and posted the submission to Figshare.com on April 11, 2014, after the submission was returned without review.

See also:  Quorum Sensing Determines the Choice of Antiphage Defense Strategy in Vibrio anguillarum

6/25/16 Excerpt: Quorum sensing links the physiology of energy-dependent reproduction and virus-driven energy theft from the microRNAome of and light organ of bobtail squid to the bull sperm microbiome, which links microRNAs in breast milk to human brain development. The bacteria that populate the light organ have already been linked by Bonnie Bassler’s group and Margaret McFall-Ngai’s group to everything known about the physiology of energy-dependent reproduction in all living genera.

Alternative splicing of pre-mRNA

Energy-dependent de novo creation and neurogenesis

See also: Tasting light links energy from creation to adaptation

Developmentally defined forebrain circuits regulate appetitive and aversive olfactory learning

reported as: When neurons are ‘born’ impacts olfactory behavior in mice

My summary:

The de novo creation of different cell types is placed into the context of their energy-dependent birth and the transgenerational epigenetic inheritance of molecular mechanisms that link virus-driven energy theft to all pathology via olfaction, food odors, and human pheromones.

See for comparison: Metabolism and neurogenesis

…it seems quite obvious that cellular metabolism determining for example the cell’s energy status will be linked to NSPC activity and neuronal differentiation processes, as cell division and differentiation are associated with an increase in cell volume and biomass production and require substantial amounts of energy for DNA replication and organelle synthesis [7].

See also: Extensive variability in olfactory receptors influences human odor perception

…the underlying amino acid sequence can vary slightly for each of the 400 receptor proteins, resulting in one or more variants for each of the receptors.

See my comments:

1) The truth revealed in the context of amino acid substitutions is that the theory of mutation-driven evolution does not make sense and it never did.

See for example: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

“…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution.”

One reason you may not know this yet is that you were taught to believe in a theory that was never supported by experimental evidence from any species.
See for review: An experimental test on the probability of extinction of new genetic variants.

2) For contrast, note the insistence by the moderator of the International Society for Human Ethology’s yahoo group. He thinks that random mutations are the substrates on which directional natural selection acts. This is what happened when I told him that natural selection is for food:

https://groups.yahoo.com/neo/groups/human-ethology/conversations/topics/48182

Jay R. Feierman, best known to me for his ridiculous question: “What about birds?” wrote:

“It is very sad for me to see that when several different people on this group, all with doctorate degrees, tell you that you are not correct, you don’t consider that they might be telling you something helpful. Instead, you respond with arrogance and ignorance. I’ll add my voice to the other people on this group who have told you that you are not correct in terms of your understanding of what “variation” means in Darwinian biological evolution and what is doing the selecting. Variation is not nutrient availability…”

All experimental evidence of biologically-based energy-dependent cause and effect has proved that Jay R. Feierman and others like him are biologically uninformed and that they choose to remain that way. This evidence from December 2012 shows that nutrient availability is the only variant that can be directly linked from the energy-dependent physiology of reproduction in bacteria to neurogenesis in the human brain!

See also: No two people smell the same

A difference at the smallest level of DNA—one amino acid on one gene—can determine whether you find a given smell pleasant.

See also: Human-specific genomic signatures of neocortical expansion

 My unedited comment:

The genomic signatures are energy-dependent and biophysically constrained by the availability of nutrients. Supercoiled DNA links what is known about nutritional epigenetics to all cell type differentiation in all living genera.

See: Metabolism and neurogenesis

  “…it seems quite obvious that cellular metabolism determining for example the cell’s energy status will be linked to NSPC activity and neuronal differentiation processes, as cell division and differentiation are associated with an increase in cell volume and biomass production and require substantial amounts of energy for DNA replication and organelle synthesis [7].”

I have access to this excellent review on the subject.

See for comparison: [MODERATOR NOTE: Edited for publishing. jrf]

RNA-mediated.com

Now that Clarence Williams is back and jrf is again editing the responses he allows me to post, I hope everyone will see more than 800 examples of what they have missed.

The examples link energy-dependent epigenetically effected alternative RNA splicing from amino acid substitutions such as BDNF Val66Met and COMT Val158Met to cell type differentiation in all cell types of all living genera via what is known about biophysically constrained biologically-based cause and effect.

In the context of what is known about animal models, Samir et al (2016) published: MicroRNAs in the Host Response to Viral Infections of Veterinary Importance MicroRNAs in the Host Response to Viral Infections of Veterinary Importance

 Many people are now aware of the role that virus-driven energy theft plays in all pathology . . ..

Feierman’s passive/aggressive ignorance and his editing of my comments has reached peak efficiency. I do not expect any attempt to contribute to discussion to appear without his editorial omissions of my content.

He exemplifies academic suppression at its finest, and has done that for more than a decade. His legacy of ignorance may be historically significant. His question “What about birds?” was answered by researchers who linked epigenetic effects of nutrients and pheromones to chromosomal rearrangements in white-throated sparrows, which led others to look for, and to find, evidence of chromosomal rearrangement and biodiversity in other species.

See: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes

…our results illustrate a detailed chain of events linking a chromosomal rearrangement to changes in overt social behavior.

Their results were perfectly predictable, and so were the Nobel Prize winning results of these two researchers.

  1. Ben Feringa (2016 Chemistry)
  2. Yoshinori Ohsumi (2016 Physiology or Medicine)

1) Dynamic control of chirality and self-assembly of double-stranded helicates with light Feringa with co-authors (2016)

2) Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates Ohsumi with co-authors (2016)

The works, cited above, predictably linked the works of these two 1933 Nobel Prize-winner to everything currently known about biophysically constrained energy-dependent RNA-mediated protein folding chemistry

  1. Thomas Hunt Morgan (Physiology or Medicine 1933)
  2. Erwin Schrodinger (Physics 1933)

1) Thomas Hunt Morgan (September 25, 1866 – December 4, 1945)[1] was an American evolutionary biologist, geneticist, embryologist, and science author who won the Nobel Prize in Physiology or Medicine in 1933 for discoveries elucidating the role that the chromosome plays in heredity.[2]

2) Schrodinger monograph (1944) What is Life?

Thermodynamic cycles of protein biosynthesis and degradation link Schrodinger’s claims about higher temperatures from autophagy to nutrient energy-dependent fixation of RNA-mediated amino acid substitutions and all cell type differentiation in humans via transgenerational epigenetic inheritance.  Everything known to all serious scientists about all cell type differentiation suggests that our immune system typically functions at it best when the supply of nutrients is linked from natural selection for codon optimality to ecological adaptation via the nutrient energy-dependent pheromone-controlled physiology of reproduction.

See also: When neurons are ‘born’ impacts olfactory behavior in mice
My summary: The de novo creation of different cell types is placed into the context of their energy-dependent birth and transgenerational epigenetic inheritance of the molecular mechanisms that link virus-driven energy theft to all pathology via olfaction, food odors, and human pheromones.
See also: TET proteins drive early neurogenesis
All neurogenesis is energy-dependent and biophysically constrained by RNA-mediated protein folding chemistry. Energy drives neurogenesis.
Proteins do not evolve. If they did, biologically uniformed theorists could claim that virus-driven energy theft linked mutated proteins to the evolution of the human brain without linking the physiology of reproduction to behavior. Simply put, as others have learned sex is a biological variable.

Addressing sex as a biological variable

Each new misrepresentation of biophysically constrained cell type differentiation outside the context of energy-dependent differences or sex as a biological variable must be viewed in the context of how theorists must continue to try to deceive those who might otherwise become serious scientists.
In this case, the journal article about the TET proteins, Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling, claims: “…Wnt3 was shown to activate Nodal expression directly through its proximal epiblast enhancer at the gastrulation stage (58, 59).
58. Blaschke, K., Ebata, K. T., Karimi, M. M., Zepeda-Martinez, J. A., Goyal, P., Mahapatra, S., et al. (2013). Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. Nature, 500(7461), 222-226.
59. Hashimoto, H., Pais, J. E., Zhang, X., Saleh, L., Fu, Z.-Q., Dai, N., et al. (2013). Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA. [Letter]. Nature.
If you are not told that the epiblast enhancers must first link nutrient energy-dependent changes in base pairs to cell type differentiation via RNA-mediated amino acid substitutions before the structure of functional proteins can be linked to anything else, you are less likely to learn that fixation of the substitutions in organized genomes only occurs via the physiology of reproduction. The pheromone-controlled physiology of reproduction links the metabolism of nutrients to all morphological and behavioral diversity in species from microbes to humans via the conserved molecular mechanisms of transgenerational epigenetic inheritance.
There is no question that transgenerational epigenetic inheritance is nutrient-dependent and pheromone-controlled is species from microbes to humans. That fact is now appearing in articles co-authored by the guest editors of a special issue of “Nutrients” who invited me to submit this review of nutritional epigenetics.

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

My invited review was returned without review. Since then, one of the guest editors incorporated my claims into this: Insights from Space: Potential Role of Diet in the Spatial Organization of Chromosomes Published: 10 December 2014

The other guest editor incorporated my claims into this: The Interaction between Epigenetics, Nutrition and the Development of Cancer  Published: 30 January 2015

Many academics clearly cannot be trusted with accurate representations of biophysically constrained biologically-based cause and effect. Unless they have a record of accurate representations they are forced to try to establish a record after-the-fact. For example, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. This is the 2013 published review that led Justin O’Sullivan and Lynnette Ferguson to request the invited review of nutritional epigenetics, which they returned without review.

My model was cited in Role of olfaction in Octopus vulgaris reproduction

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

It was also cited in Two fatty acyl reductases involved in moth pheromone biosynthesis (see #10)

Studies over the last two decades have pinpointed that the epigenetic effect of pheromone-driven adaptive evolution is one of the major factors driving the successful diversification of Lepidopteran insects10. In moths, a few substitutions in critical amino acids in the key pheromone biosynthetic enzymes are sufficient to create a novel pheromone component11,12.

If others had not cited my model, which is a refutation of neo-Darwinian pseudoscientific nonsense, there would be no record of experimentally established facts that link energy-dependent changes in the microRNA/messenger RNA balance to all cell type differentiation via RNA-mediated amino acid substitutions in all invertebrates and vertebrates.

fruit-dove

Theories vs facts about polycombic adaptation

See: Demoncrats fight polycombic ecological adaptation

Exosomes as miRNA Carriers: Formation–Function–Future

Important aspects will be highlighted as a take-home message (THM) at the end of each paragraph.

THM: Extracellular vesicles transport miRNA in a paracrine and endocrine manner. Questions regarding the cellular options of producing either microvesicles or exosomes and their difference in miRNA composition and number are still unknown.

In my 2014 invited review, the four F’s, Formation–Function–Future and Copulation were included in details about how the nutrient energy-dependent de novo creation of microRNAs must be linked to nutritional epigenetics. My invited review was returned without review by the guest editors of a special issue of “Nutrients.”
I realized the guest editors had “baited me” into providing them with all the available current information and published my submission to Figshare. That’s how I show the level of deception that biologically uninformed theorists still use to obfuscate what is known to serious scientists about biologically-based cause and effect.

See for example: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (April 10, 2014)

Abstract: “This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.”

Lynnette Ferguson, was one of two guest editors that invited my review.
 
She is the co-author of The Interaction between Epigenetics, Nutrition and the Development of Cancer This article belongs to the Special Issue NutritionalEpigenetics
 

Conclusion:

…it is imperative to understand the implications of diet on epigenetic modifications, and the effect of those modifications on the development of cancer today and in future generations. Such an understanding and an appropriate resultant response would help decrease the level of risk in future generations.

There would be no future generations if diet could not be epigenetically linked from metabolism to the pheromones that control the physiology of reproduction in species from microbes to human via energy-dependent changes in the microRNA/messenger RNA balance. The microRNA/messenger RNA balance biophysically contrains RNA-mediated protein folding chemistry.

Protein folding chemistry links energy-dependent changes from angstroms to ecosystems in all living genera via the innate immune system and fixation of RNA-mediated amino acid substitutions in supercoiled DNA. Supercoiled DNA exemplifies natural section for energy-dependent codon optimality, but theorists will not accept that fact. They would rather believe that the mutations in DNA are naturally selected and that mutation-driven evolution automagically occurs outside the context of energy or the virus-driven energy theft that causes all mutations and all pathology.

See also: The developmental basis for the recurrent evolution of deuterostomy and protostomy

This scenario challenges the assumed value of extant blastoporal behaviours for explaining the evolutionary origin and diversification of Bilateria that has been presumed for over 100 years4,5,6,7,9,10,11. Freeing the constraint that the mouth and anus have a necessary association with the embryonic blastopore will help in understanding the developmental events underlying the evolution of an alimentary canal5,20,21,50, and ultimately the appearance and diversification of bilaterian body plans.

All scenarios that failed to link energy-dependent behavior to the physiology of reproduction and also failed to link virus-driven energy theft to all pathology have always been based on questionable assumptions. The assumptions fall outside the context of Darwin’s “conditions of life,” which require links from what organisms eat to signaling and sensing and the behavior of other organisms.

For example, Schrodinger (1944) linked excretion from mammals to sunlight as the source of anti-entropic virucidal energy used to support all ecosystems. All serious scientists have done that since Thomas Hunt Morgan won the 1933 Nobel Prize in Physiology or Medicine for linking chromosomes to transgenerational epigenetic inheritance long before most people understood what the term autophagy means.

Alternative splicing of pre-mRNA

The futility of The Battlefield FB group

Apparently, Paul Hartley blocked me from further discussion of his OP about dinosaurs and gladiators before I could ask if he thought “The Battlefield” is a “false flag” group. Does anyone else think that?
 

If so, do you think it can survive publication of experimental evidence that links responsive supramolecular systems to stepwise changes in the assembly of metal complexes via induction of a light-driven rotary motor scaffold akin to the bacterial flagellum of P. fluorescens?

See: Dynamic control of chirality and self-assembly of double-stranded helicates with light

Others are claiming that partial unwrapping of the supercoiled DNA complex precedes the photoisomerization steps, which link energy-dependent autophagy to inversion of the chirality in helicates. That explains how energy-dependent RNA-mediated isomerization establishes the difference between metastable and stable helicates, which links amino acid substitutions to supercoiled DNA, which protects all organized genomes from virus-driven entropy. For example, supercoiled DNA protects the organized genomes of dinosaurs and gladiators from stress-linked pathology until stress-linked changes in pH overcome the ability of the innate immune systems to protect the organized genomes via the light-induced changes in hydrogen-atom transfer in DNA base pairs in solution.
See for comparison: Team combines quantum physics and photosynthesis to make discovery that could lead to highly efficient solar cells

They claim plants evolved to control responses to the sun’s biological energy. As proof of concept their “…design incorporates a heat engine photocell that absorbs photons from the sun and converts the photon energy into electricity.”

Via the comparison of two simple quantum mechanical photocell systems, they found that “…by simply incorporating two photon-absorbing channels, rather than only one, the regulation of energy flow emerges naturally within the photocell.”

They linked the natural emergence of the energy flow in their design to the natural energy of photosynthesis in plants in an attempt to explain how green became the predominant color of plants on Earth. Others found molecular structures that prevent death via the accumulation of excess energy in plants.

The design of the molecular structure of their quantum heat engine photocell is similar to “…the structure of photosynthetic molecules that incorporate pairs of chlorophyll.” But wait. They claimed that the plants evolved molecular mechanisms after the natural emergence of energy flow was linked to photosynthesis and molecular structures that prevent death caused by the accumulation of excess energy.When I see such a convoluted representation of energy-dependent biologically-based cause and effect that does not include any mention of virus-driven energy theft or the physiology of reproduction, I am inclined to call researchers like this “biologically uninformed science idiots.”Many people hate it when I do that. What would you call them? But some of them are plagiarists, too.

See: Modern Science refutes the Evolutionary theory

Tomi Aalto’s blog is a continuation of his plagiarism. His posts can be compared to more than 800 of mine on my domain.

The difference is that Suzan Mazur acknowledged RNA-mediated.com as an information source in her book: Royal Society: The Public Evolution Summit

From page 3: “Some of the social momentum over the last year, in particular, has come via coverage of the evolution discourse in a flurry of books and from these diverse venues…”

James Kohl — RNA-mediated.com

In “Darwin’s Children” (2003) Greg Bear also acknowledged me and the International Paleopsychology Project, where I first encountered him and Eshel Ben-Jacob, who died last year. See this tribute to Eshel’s works.

He mastered the concept of energy-dependent autophagy and linked everything known about Schrodinger’s anti-entropic virucidal energy of sunlight to the nutrient-dependent physiology of pheromone-controlled reproduction in species from microbes to humans.
Theorists still hate it when that happens, and they continue to tell others who are biologically uninformed that not enough is known to link virus-driven energy theft to all pathology.

What does Tomi Aalto, or any other plagiarist hope to accomplish by taking bits and pieces of my works, or the works of others, without the ability to link the energy-dependent de novo creation of G protein-coupled receptors from energy as information to all biodiversity and also link virus-driven energy theft to all pathology? That inability to link top-down causation to any model of biologically-based cause and effect led to this criticism of my 2013 review.

Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

Would it not be more appropriate for others who are not atheistic antagonists to support my claims by citing and discussing my works, rather than make ongoing attempts to establish themselves as experts?

See for examples of what is expected of other serious scientists.

Role of olfaction in Octopus vulgaris reproduction

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

Two fatty acyl reductases involved in moth pheromone biosynthesis also cites Kohl (2013) see #10

Studies over the last two decades have pinpointed that the epigenetic effect of pheromone-driven adaptive evolution is one of the major factors driving the successful diversification of Lepidopteran insects10. In moths, a few substitutions in critical amino acids in the key pheromone biosynthetic enzymes are sufficient to create a novel pheromone component11,12.

Re: Tomi Aalto’s plagiarism and the plagiarism of others.


Larry Kisner Sr. suggested I contact Kevin Anderson in an attempt to publish what I have already published. He also refused — and Mark Armitage ignored my requests — to provide the slide that shows fluorescence in dinosaur osteocytes.

See my comment on the video by Mark Armitage. See also: Future Projects
 
The Influence of Carbon Dioxide Enhancement on Plant Growth
Thermoregulation in Honey Bees
Fossils of the Coconino Sandstone
Biochemistry and Taxonomy in Pine Trees
The Formation of Multiple Tree Rings in Bristlecone Pine Trees
 

Each of these projects focuses on aspects of my published and unpublished works that link the sun’s anti-entropic virucidal energy to RNA-mediated amino acid substitutions and biophysically constrained cell type differentiation in species from microbes to humans.

See for example: What is life when it is not protected from virus driven entropy  (video 6:37 minutes)

Abstract:

The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

See also: Metabolic Phenotyping Research

Excerpt: SARCASM ALERT

7. They will claim that the Extended Evolutionary Synthesis will have explanatory power when it automagically evolves into a model of top-down causation that links physics and chemistry to the conserved molecular mechanisms of biologically-based cause and effect, which serious scientists have detailed during the past century.

See for comparison:

Analysis of Viral and Cellular MicroRNAs in EBV-Infected Cells

Dual genomes: exposing the evolution industry

Pheromones and longevity in worms (and flies)

I posted this to one of my OPs on “The Battlefield,” which means I may be the next to go. Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks
 

For comparison to what is known about the de novo creation of genes in mollusks, Anna Di Cosmo’s group cited my most recent review in Role of olfaction in Octopus vulgaris reproduction.

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000). — p. 61

The facts link my model to biologically-based cause and effect from energy-dependent changes in angstroms to ecosystems in all living genera via the de novo creation of the genetic code. See also: Junk DNA’ Used To Sort Species

Now watch Lenski’s group claim that different species of viruses evolved in one month. Biologists watch speciation in a laboratory flask
Nutrient energy-dependent pheromone-controlled speciation can now be observed in the context of fluorescence, which links ecological variation to morphological and behavioral diversity to chromosomal rearrangements in C. elegans compared to P. pacificus, a predatory nematode with teeth. Researchers find chemical tag that locks chromosomes together during meiosis 

The ENEA study proposed that the image may have been created by an intense source of light, but no man-made light would produce the required strength.

Serious scientists have linked femotosecond blasts of UV light to RNA-mediated DNA repair and the repair has been linked via the natural fluorescence in DNA from dinosaur osteocytes to the weekend resurrection of the bacterial flagellum. One could look at the evidence in the discovery at Christ’s tomb from that perspective given the intensity of light energy as information that might be required to Resurrect Him.
For comparison, Lenski’s group has placed everything he knows into the context of evolved species of viruses during a month-long experiment that failed to include anything known about biophysically constrained energy-dependent RNA-mediated cell type differentiation in any living species. Again, see: Biologists watch speciation in a laboratory flask
The bottom line is always whether you choose to believe in theorists or in the evidence of biologically-based cause and effect — no matter when that evidence is discovered or where it is found.

See: Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees

Natural selection for energy-dependent codon optimality is the only obvious link to the de novo creation of olfactory receptor genes. And Svante Paabo is the senior author. Here he is again, supporting my model with others who understand the role of microRNAs. MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates

Does everyone understand why Bill Ludlow blocked me after I commented on his OP from “The Battlefield?” about this:

Scientists Seek to Update Evolution

See also: Tertiary alphabet for the observable protein structural universe
From the journal article: “…the frequency of amino acids in different secondary-structural environments is closely related to thermodynamic propensities (20–24).”
From the news report: “Since protein structural states are really conformational ensembles, the language of statistical mechanics is most appropriate for describing their behavior.”
This is the language they use: “…we find that the emergent sequence variability is often in close agreement to the evolutionary variability…”
Instead of linking sunlight from thermodynamic cycles of energy-dependent protein biosynthesis and degradation to biophysically constrained cell type differentiation and all RNA-mediated biodiversity, they link emergence to evolution.
Welcome again to the world of biologically uninformed theorists. This time, “…we systematically decompose the known protein structural universe into its basic elements, which we dub tertiary structural motifs (TERMs).”
The ability to take everything known to serious scientists and put it back into the context of unintelligible theories via use of terms like tertiary structural motifs far surpasses the ability of serious scientists to make sense of their pseudoscientific nonsense. Thus, the pseudoscientific nonsense will continue to kill us all.
See for comparison: The Pangenome: Are Single Reference Genomes Dead?

…when Tettelin, then at the Institute for Genomic Research (TIGR), and his colleagues compared eight isolates of Streptococcus agalactiae (or group B Streptococcus, GBS), they found not only the small, within-gene variations predicted by conventional genetics, but an average of 33 completely new genes with every new genome sequenced. “It was a shock,” says Tettelin. “We saw there were many regions—relatively large regions—of diversity.”

All that diversity is energy-dependent and linked from the pheromone-controlled physiology of reproduction to all  morphological and behavioral phenotypes in all living genera.

Thanks to Anna Di Cosmo for sharing this example of energy-dependent de novo transcriptome assembly.

Abstract conclusion:

The use of de novo transcriptome assembly and well-designed in silico protocols proved to be a robust approach for surveying and mining large sequence data in a wide range of non-model mollusks. The data presented herein constitute only a small fraction of the information retrieved from the analysed molluscan transcriptomes, which can be promptly employed in the identification of novel genes and gene families, phylogenetic inferences, and other studies using molecular tools. As such, our study provides an important framework for understanding some of the underlying molecular mechanisms involved in molluscan body plan diversification and hints towards functions of key developmental genes in molluscan morphogenesis.

No serious scientist I know examines morphogenesis outside the context of feedback loops that link odor and pheromones to the physiology of reproduction in species from microbes to humans via the de novo creation of G protein-coupled receptors (GPCRs). How many pseudoscientists do you know who skip past the de novo creation of GPCRs and proceed to link mutations from natural selection to evolution outside the context of everything known to serious scientists about biologically-based cause and effect (i.e., energy-dependent biodiversity)?The lack of discussion and/or support from other creationists for my presentations of accurate information like this may suggest to others that this is a “false flag” group. Note that after I blocked those who I know participate in other “false flag” groups, there has been no discussion of my OPs. If you tried to evaluate the content presented here, would you get the impression that this is a group in which the admins are Creationists? When did you realize the de novo creation of genes for olfactory receptors must precede the de novo creation of photoreceptors to link chemotaxis and phototaxis to energy-dependent cell type differentiation, which is our only protection from the viral apocalypse?

See: Pterosaurs Hijack Royal Society Evo Meeting

See also: Royal Society: The Public Evolution Summit

Page 11- 12 Re: … evolution of genome invading RNA networks that edit host genomes.

… Witzany is organizing a conference symposium for July 2018 “Evolution-genetic innovations without error replication

He is the author of Life is physics and chemistry and communication.

Abstract:

Manfred Eigen extended Erwin Schroedinger’s concept of “life is physics and chemistry” through the introduction of information theory and cybernetic systems theory into “life is physics and chemistry and information.” Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language. However, the basics of scientific knowledge changed dramatically within the second half of the 20th century. Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life.

The claims about quasispecies and hypercyclesthat dominate molecular biology and virology should have long ago long before now have been placed into the context of all reviews of neo-Darwinian pseudoscientific nonsense.

See for example: Major Evolutionary Blunders: Imagining That Life Is Only Chemistry

See also: “I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries” (p. 732).  — Lewis Thomas as cited in The Scent of Eros: Mysteries of Odor in Human Sexuality

Physics

Controlled amino acid treatment of all pathology

Amino acid studies.com
Excerpt:

One of the cancer treatments that seems to be proving effective over time is CAAT: Controlled Amino Acid Treatment. CAAT works by restricting certain amino acids from the diet to combat the growth and reproduction of the cancerous cells.

Excerpt:

doctors can now actively battle cancers, using the best weapons possible, natural amino acids, which are actually designed to make changes in the body.

The trick has been to understand which changes are beneficial to cancer (or disease) sufferers, and which are not.

The trick is to understand how energy-dependent RNA-mediated protein folding chemistry is linked to biophysically constrained supercoiled DNA, which prevents virus-driven energy theft from causing all pathology. That understanding has not been made possible because it undermines the mutually supportive associations between politics and academia.
The Real War on Science(1) has gone virtually unnoticed by anyone who is not already (2) Combating Evolution to Fight Disease

(1)  Excerpt:

The Left’s most rigid taboos involve the biology of race and gender, as the Harvard psychologist Steven Pinker chronicles in The Blank Slate. The book takes its title from Pinker’s term for the dogma that “any differences we see among races, ethnic groups, sexes, and individuals come not from differences in their innate constitution but from differences in their experiences.” The dogma constricts researchers’ perspective—“No biology, please, we’re social scientists”—and discourages debate, in and out of academia.

(2)

Darwin probably anticipated the insemination of population genetics that led to the bastardization of his detailed observations in the “Modern Synthesis.” He politely insisted that ‘conditions of life’ be considered before natural selection.

There are two ‘conditions of life.’ It is nutrient-dependent and pheromone-controlled. Rosenberg and Queitsch now note the work with Dobzhansky’s rarely acknowledged claim: “I am a creationist and an evolutionist.” They also declare the need for “Deep understanding of the mechanisms that generate variation at the molecular level…”

Deep understanding of the ‘conditions of life’ does not come from theory.

Problems with the “modern synthesis” now lead us back to the facts about biologically-based cause and effect that Darwin and Dobzhansky approached with humility, which are the same biological facts that evolutionists approached with ignorance about behavioral affects and the arrogance that accompanies that ignorance. Rosenberg and Queitsch echo the sentiments of those who have been subjected to academic suppression.

Clearly, however, “nothing in evolution makes sense except in the light of biology” is not an exaggeration. It is a common sense statement about the biologically plausible genesis of functional cell types. Population genetics and evolutionary theories abandoned the biophysical constraints of ecological variation and the physiology of reproduction, which enable epigenetically-effected nutrient-dependent pheromone-controlled receptor-mediated ecological adaptations and species diversity via the complexities of protein folding and niche construction.

It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution.

Let’s start with sex as a biological variable, shall we? Addressing sex as a biological variable
Which amino acid substitutions stabilized the sex differences in cell types at the advent of sexual reproduction in yeasts? What happened to stabilize the organized genomes of all living genera that sexually reproduce? What else besides the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria could be used as a basis for the required links from energy-dependent changes in angstroms to ecosystems that do not seem to be caused by virus-driven energy theft and mutations?
See also: From Fertilization to Adult Sexual Behavior

See also: Gender-Specific Association of Galanin Polymorphisms with HPA-Axis Dysregulation, Symptom Severity, and Antidepressant Treatment Response
See also: Single-nucleotide polymorphism rs948854 in human galanin gene and multiple sclerosis: a gender-specific risk factor
Controlled amino acid treatments will take advantage of everything known to serious scientists about energy-dependent links from angstroms to ecosystems via RNA-mediated cell type differentiation. Most of what is known has only recently confirmed the works that led to the 1933 Nobel Prize in Physics (Schrodinger and Dirac) and the Prize in Physiology or Medicine (Morgan).
See for example: Fluorescence Correlation Spectroscopy — Going Beyond the Diffraction Limit
Excerpt:

In the simplest possible case, employing only one excitation wavelength, the sequence consists first of an excitation laser pulse (blue), followed by a slightly delayed STED laser pulse (red). The non-quenched emission light can then be collected, leading to a fluorescence decay obtained under STED conditions. The second part of the sequence features only the excitation pulse and the resulting decay curve is thus collected under confocal conditions.

Conclusion:

Furthermore, following the gradual changes in diffusion coefficient as a function of observation area size can provide insights into the organization and dynamics of the cell membrane beyond the diffraction limit. The method can be expanded for studies involving more than one fluorescent species by, for example, adding more excitation lasers to the PIE pulse pattern. In addition to cell membrane investigations, PIE-STED-FCS can also be applied to any research area where precise observation of the diffusion times of fluorescent species with high lateral resolution is desirable or required, such as membrane permeability or protein mobility studies.

Femtosecond blasts of ultraviolet light have already been linked to energy-dependent DNA repair. See: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
Energy-dependent RNA-mediated DNA repair is clearly linked from the physiology of reproduction to supercoiled DNA and healthy longevity. Virus-driven energy theft is linked to all pathology. Researchers are on the verge of learning which viruses are causing the pathology linked from negative supercoiling to species-specific tissue type-specific pathology in all cell types of all individuals of all living genera.
But you will still hear claims from theorists that not enough is known about how to prevent all pathology. Once everyone else learns how to prevent all pathology via controlled amino acid treatments, the claims of theorists will be exposed as the most ignorant of all claims since the Nobel Laureates from 1933 exposed the pseudoscientific nonsense touted by those who invented neo-Darwinism.
See also: Using light to map the circuitry of the brain

“This allows the image to be mapped to different frequency bands – like tuning a radio,” explains Zhou. “The delay separates the images for the light to detect different optical frequencies at the same time.”

My comment: It will allow all serious scientists to examine a detailed model of how energy-dependent RNA-mediated protein folding chemistry links base pairs from SNPs and species-specific nutrient-dependent pheromone-controlled cell type differentiation from fertilization to adult sexual behavior during life history transitions.
See for example: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
 

IMG_3010

Survivors of RNA-mediated terrorism

In Darwin’s Radio and Darwin’s Children, Greg Bear predicted there would be ecologically adapted survivors of the forthcoming viral apocalypse.  Could his “raw insight” help to save you, or help to save any of your loved ones who are not already dead? Or, is it too late for us all?
See:The Darwin Code: Intelligent Design without God
Excerpt: 

Once again, evolution is a fresh territory, much larger than anyone thought. The Darwin code–the key to all of our new maps–has yet to be deciphered in its most important aspect–how it stores up and then releases the knowledge it has derived from experience.

The experience-dependent knowledge is stored as energy-dependent naturally occurring fluorescence in the supercoiled DNA of all cell types in all species from microbes to humans.
See: Quorum Sensing Controls Adaptive Immunity through the Regulation of Multiple CRISPR-Cas Systems
Excerpt: This nascent immunity is further reinforced by the elevated interference invoked by spacers from the three different systems.
Quorum Sensing Controls Adaptive Immunity through the Regulation of Multiple CRISPR-Cas Systems / Credit: Molecular Cell 2016 Patterson et al
Reported by Carmen Leitch as: Quorum Sensing Prods Bacteria to Increase CRISPR/Cas Immunity

“As humans, we have evolved sophisticated immune systems that enable our bodies to fight the viral infections that render us ill. Amazingly, bacteria – although single celled organisms – often possess similar adaptive immunity called CRISPR/Cas systems. But the way that these CRISPR/Cas systems function is very much different to our own immune systems,” he says.

He is lying and Carmen Leitch consistently reports the lies, which are framed within the ridiculous context of the neo-Darwinian evolution of nascent immunity. The innate immune system is nor referred to the nascent immune system except by theorists. The innate immune system is not an evolved system of nascent immunity, which theorists think they can continue to link to their theories about evolved biodiversity.
The scientific truth is known about the energy-dependent creation of the innate immune system. Theorists would rather kill us all with their ridiculous theories about how nascent immunity evolved than to admit they have always been wrong to believe in ridiculous theories of evolution.
The ab initio energy-dependent de novo creation of G protein-coupled receptors (GPCRs) clearly links the innate immune system of bacteria and humans from autophagy to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.
From February 2009 published to YouTube in 2013

See also: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Published: 15 March 2012
Excerpt: An epigenetic continuum from microbes to humans: from theory to facts

Among different bacterial species existing in similar environments,  (Palchevskiy & Finkel, 2009) appears to have epigenetically ‘fed’ interspecies methylation and speciation via conjugation (Fall et al., 2007; Finkel & Kolter, 2001; Friso & Choi, 2002). This indicates that reproduction began with an active nutrient uptake mechanism in heterospecifics and that the mechanism evolved to become symbiogenesis in the conspecifics of asexual organisms (Margulis, 1998). In yeasts, epigenetic changes driven by nutrition might then have led to the creation of novel cell types, which are required at evolutionary advent of sexual reproduction (Jin et al., 2011). These epigenetic changes probably occur across the evolutionary continuum that includes both nutrition-dependent reproduction in unicellular organisms and sexual reproduction in mammals. For example, ingested plant microRNAs influence gene expression across kingdoms (Zhang et al., 2012). In mammals, this epigenetically links what mammals eat to changes in gene expression (McNulty et al., 2011) and to new genes required for the evolutionary development of the mammalian placenta (Lynch, Leclerc, May, & Wagner, 2011) and the human brain (Zhang, Landback, Vibranovski, & Long, 2011).

A gene that codes for the mammalian olfactory receptor, OR7D4, links food odors to human hunger, dietary restraint, and adiposity (Choquette et al., 2012). OR7D4 exemplifies a direct link1 from human social odors to their perception (Keller, Zhuang, Chi, Vosshall, & Matsunami, 2007) and to unconscious affects2 on human behavior associated with human olfactory-visual integration (Zhou, Hou, Zhou, & Chen, 2011); human brain activation associated with sexual preferences (Savic, Heden-Blomqvist, & Berglund, 2009), human learned odor hedonics; and motor function (Boulkroune, Wang, March, Walker, & Jacob, 2007). Insect species exemplify one starting point along an evolutionary continuum from microbes to humans that epigenetically links food odors and social odors to multisensory integration and behavior.

See also: Ask Carmen Leitch why she has never mentioned this Labroots virtual conference presentation or any of my published works.


The ultimate insult to the integrity of all serious scientists is to take this model of biologically-based cause and effect and link it to prurient self interests in :

See also:

  1. Nutrient-dependent/pheromone-controlled adaptive evolution: a model
    James Vaughn Kohl, Socioaffect Neurosci Psychol, 2013
  2. Criticisms of the nutrient-dependent pheromone-controlled evolutionary model
    Andrew Jones, Socioaffect Neurosci Psychol, 2014
  3. Introductory Editorial to ‘The Neuroscience and Evolutionary Origins of Sexual Learning’
    Adam Safron et al., Socioaffect Neurosci Psychol, 2012
  4. Sexual addiction: insights from psychoanalysis and functional neuroimaging
    Harold Mouras et al., Socioaffect Neurosci Psychol, 2012

In the context of a world-view touted by biologically uninformed theorists, we see how virus-driven energy theft could easily cause the death of us all despite the facts about quorum sensing that are known to serious scientists. Quorum sensing is nutrient-dependent and pheromone-controlled via autophagy, which links quorum sensing to supercoiled DNA via energy-dependent metabolic networks and genetic networks.
That message is difficult to convey in non-technical language, which suggests it may not ever be heard in the context of effective communication because people have been trained not to listen.
See also: 

See also:  Susan M Rosenberg, Ph.D.

One of the human, the yeast and fly RecQ homologues, appear to play one specific role in genetic recombination in cells. Surprisingly, we found that E. coli RecQ plays the opposite role, and thus exemplifies a second paradigm for the in vivo function of RecQ-family proteins. We are investigating whether any of the human homologues function via the E. coli RecQ paradigm, and the molecular basis of RecQ action in vivo as a model for human oncogenesis. We are pursuing other promising bacterial homologues of human cancer proteins to learn their mechanisms of action first in the simpler, more tractable bacterial system to provide mechanisms and models for the molecular bases of cancer.

The E. coli RecQ paradigm links the nutrient energy-dependent biophysically constrained chemistry of RNA-mediated protein folding from changes in base pairs to amino acid substitutions in supercoiled DNA that protect the organized genomes of all living genera from virus-driven energy theft and all pathology. There is a model for that!
Nutrient-dependent/pheromone-controlled adaptive evolution: a model
The model is also a refutation of neo-Darwinian pseudoscientific nonsense.
Criticisms of the nutrient-dependent pheromone-controlled evolutionary model
Excerpt:

Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. It was a mistake to let such a sloppy review through to be published.

Andrew Jones, BA

Editor’s note

The 2013 review article by James Vaughn Kohl published in Socioaffective Neuroscience & Psychology and criticized in the above Letter to the Editor was subjected to standard peer review and the revised version was accepted by me after it had been accepted by both reviewers.

My comment: There is still no other model of biologically-based cause and effect for comparison.

See also:

 
See also: Small non-coding RNAs associated with viral infectious diseases of veterinary importance: potential clinical applications

Alternative splicing of pre-mRNA

RNA-mediated "repurposing" is autophagy

Autophagy (or autophagocytosis) (from the Ancient Greek αὐτόφαγος autóphagos, meaning “self-devouring”[1] and κύτος kýtos, meaning “hollow”[2]) is the natural, regulated, destructive mechanism of the cell that disassembles unnecessary or dysfunctional components.[3]

RNA-mediated “repurposing” is nutrient-dependent and pheromone-controlled

RNA-mediated repurposing in microbes and adaptations in primate brains

Selective reporting of inferences: examples of pseudoscience

Autophagy Pioneer Wins Nobel

See my comments:

..autophagy, the process by which a cell recycles unnecessary components. “His discoveries opened the path to understanding the fundamental importance of autophagy in many physiological processes, such as in the adaptation to starvation or response to infection…

How much more can be done without claiming that the energy-dependent changes link natural selection to codon optimality and codon optimality links fixed RNA-mediated amino acid substitutions to the stability of all cell types in all living genera via supercoiled DNA. The supercoiled DNA links ecological variation to ecological adaptation via the physiology of reproduction, which is the only way I know to prevent virus-driven energy theft from being transgenerationally inherited as it is with the Zika virus.
Research delivers ground-breaking insights into evolution by studying transcription termination in archaea
From the title above, would anyone recognize that this is a second report on the research reported in The Scientist on August 1, 2016 as Wanted: Transcriptional Regulators
The journal article was published on April 8, 2016. See Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria
Conserved molecular mechanisms of energy-dependent autophagy are obviously the link from virus-driven nutrient-dependent pheromone-controlled antibiotic resistance in bacteria to supercoiled DNA, which protects human infants from the transgenerational epigenetic inheritance of Zika virus damage.
But, in Research delivers ground-breaking insights into evolution by studying transcription termination in archaea we are told that…

In order to describe the diversity of life, science differentiates, for example, between the plant and animal kingdoms.

What differences does science introduce to remove the molecular mechanisms of autophagy from archea before linking them to cell type differenitation in all other living genera?